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The series focuses on the Muslim community in the fictional prairie town of Mercy, Saskatchewan (population 14,000).
Sarah and Rayyan work at cross purposes to help each other come to terms with Sarah's divorce.
When Amaar tries to solve Rayyan's problems at work, he causes her extra stress at home.
After blowing out the old fuse box in their house, Amaar tries to impress Rayyan by playing Mr. Handyman but has to secretly enlist Sarah’s do-it-yourself expertise to get the job done. Rayyan becomes suspicious of his sudden upsurge in Mr.-Fix-it skills and volunteers Amaar to fix Fred’s shower, Meanwhile, Baber and Thorne challenge each other to a fasting competition that escalates to insane heights, even for them.
Amaar needs Baber and Thorne’s cooperation to win a coveted Multi-Faith Award, but Baber and Thorne try to cut Amaar out when they discover the award comes with a cash prize. Meanwhile, Ann sets Sarah up on the worst first-date of her life, which leads to the worst second-date of her life. And Nate and Fatima team up to make a multi-ethnic sandwich.
Amaar and Rayyan’s first official dinner party as a married couple goes off the rails when Thorne’s brother Charles shows up in Mercy.
Amaar gets a sign from above in the most unexpected, yet fateful manner.
Amaar tries to get the town to support his new Mosque, but finds only disinterest and some outright derision when he reveals that his divine inspiration came from a chicken. Meanwhile, Baber is determined to prove the town isn’t ready for a new mosque by trying to get himself arrested. Sarah has a crisis of faith and considers eating bacon, while Ann suffers a crisis of love while sexting the now absent Charles Thorne.
Sarah feels undervalued by Ann and agrees to work for Darnelly’s Mayor, Glenda Beckford, not realizing that Ann’s college ‘frenemy’ has ulterior motives for hiring her. Meanwhile, Amaar is so consumed with his plans for the new Mosque, he manages to forget Rayyan’s birthday. Baber and Thorne compete for clients at the mosque/church’s last rummage sale.
When Amaar inadvertently leads everyone to believe that the new Mosque is haunted, Sarah runs damage control and suggests he and Rayyan spend the night in the Mosque to prove it’s completely ghost-free. Meanwhile, a love-struck Nate goes to extreme lengths to ask Poppy out on a date. And Thorne helps Baber overcome his irrational fear of Jinn.
In the lead up to the series finale, Amaar reveals to Baber that he plans to be the Imam of the new Mosque. In turn, Baber revolts and forms a splinter Mosque. Meanwhile, Ann is distraught over Charles’ upcoming nuptials to a younger woman and comes up with a bizarre strategy to fight for her man. And Sarah attempts to rejoin the church choir, with fiery results.
In a series finale that lets Little Mosque on the Prairie live up to it’s namesake, Amaar prepares for the grand opening of the new Mosque, while trying to get Baber to end his boycott. Charles returns to Mercy with a plan to win Ann. Sarah reaffirms her Muslim faith; and, with Mercy Anglican burnt to a crisp, Thorne finds an unexpected new home for his congregation.
